Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:35 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the ChIPpeakAnno package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPpeakAnno.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 325/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ChIPpeakAnno 3.33.2 (landing page) Jianhong Ou
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
Package: ChIPpeakAnno |
Version: 3.33.2 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ChIPpeakAnno_3.33.2.tar.gz |
StartedAt: 2023-04-12 05:17:39 -0400 (Wed, 12 Apr 2023) |
EndedAt: 2023-04-12 05:34:40 -0400 (Wed, 12 Apr 2023) |
EllapsedTime: 1021.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ChIPpeakAnno.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ChIPpeakAnno_3.33.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ChIPpeakAnno.Rcheck’ * using R Under development (unstable) (2023-02-14 r83833) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 * running under: Ubuntu 20.04.6 LTS * using session charset: UTF-8 * checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ChIPpeakAnno’ version ‘3.33.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ChIPpeakAnno’ can be installed ... OK * checking installed package size ... NOTE installed size is 19.1Mb sub-directories of 1Mb or more: data 12.6Mb extdata 5.2Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘ensembldb’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE oligoFrequency : <anonymous>: no visible global function definition for ‘oligonucleotideFrequency’ Undefined global functions or variables: oligonucleotideFrequency * checking Rd files ... NOTE checkRd: (-1) assignChromosomeRegion.Rd:133: Escaped LaTeX specials: \_ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed findEnhancers 21.333 0.264 21.597 annotatePeakInBatch 14.543 0.456 15.000 findMotifsInPromoterSeqs 13.464 0.270 13.743 summarizeOverlapsByBins 5.930 0.417 6.066 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘ChIPpeakAnno.Rmd’ using ‘UTF-8’... OK ‘FAQs.Rmd’ using ‘UTF-8’... OK ‘pipeline.Rmd’ using ‘UTF-8’... OK ‘quickStart.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’ for details.
ChIPpeakAnno.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ChIPpeakAnno ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘ChIPpeakAnno’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading in method for ‘annoGR’ with signature ‘"EnsDb"’: no definition for class “EnsDb” in method for ‘toGRanges’ with signature ‘"EnsDb"’: no definition for class “EnsDb” ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ChIPpeakAnno)
ChIPpeakAnno.Rcheck/tests/runTests.Rout
R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > require("ChIPpeakAnno") || stop("unable to load Package:ChIPpeakAnno") Loading required package: ChIPpeakAnno Loading required package: IRanges Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: GenomicRanges Loading required package: GenomeInfoDb [1] TRUE > require("BSgenome.Drerio.UCSC.danRer7") || stop("unable to load Package:BSgenome.Drerio.UCSC.danRer7") Loading required package: BSgenome.Drerio.UCSC.danRer7 Loading required package: BSgenome Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: rtracklayer [1] TRUE > require("org.Hs.eg.db") || stop("unable to load Package:org.Hs.eg.db") Loading required package: org.Hs.eg.db Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. [1] TRUE > require("org.Ce.eg.db") || stop("unable to load Package:org.Ce.eg.db") Loading required package: org.Ce.eg.db [1] TRUE > require("BSgenome.Celegans.UCSC.ce10") || stop("unable to load Package:BSgenome.Celegans.UCSC.ce10") Loading required package: BSgenome.Celegans.UCSC.ce10 [1] TRUE > require("EnsDb.Hsapiens.v79") || stop("unable to load Package:EnsDb.Hsapiens.v79") Loading required package: EnsDb.Hsapiens.v79 Loading required package: ensembldb Loading required package: GenomicFeatures Loading required package: AnnotationFilter Attaching package: 'ensembldb' The following object is masked from 'package:stats': filter [1] TRUE > require("TxDb.Hsapiens.UCSC.hg38.knownGene") || stop("unable to load TxDb.Hsapiens.UCSC.hg38.knownGene") Loading required package: TxDb.Hsapiens.UCSC.hg38.knownGene [1] TRUE > require("biomaRt") || stop("unable to load biomaRt") Loading required package: biomaRt [1] TRUE > require("reactome.db") || stop("unable to load reactome.db") Loading required package: reactome.db [1] TRUE > require("testthat") || stop("unable to load testthat") Loading required package: testthat Attaching package: 'testthat' The following object is masked from 'package:AnnotationFilter': not [1] TRUE > test_check("ChIPpeakAnno") [ FAIL 0 | WARN 4 | SKIP 6 | PASS 316 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • empty test (6) [ FAIL 0 | WARN 4 | SKIP 6 | PASS 316 ] > > proc.time() user system elapsed 165.409 3.229 170.866
ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings
name | user | system | elapsed | |
ChIPpeakAnno-package | 0 | 0 | 0 | |
ExonPlusUtr.human.GRCh37 | 3.701 | 0.236 | 3.937 | |
HOT.spots | 0.138 | 0.008 | 0.146 | |
IDRfilter | 0 | 0 | 0 | |
Peaks.Ste12.Replicate1 | 0.054 | 0.000 | 0.054 | |
Peaks.Ste12.Replicate2 | 0.008 | 0.003 | 0.012 | |
Peaks.Ste12.Replicate3 | 0.012 | 0.000 | 0.012 | |
TSS.human.GRCh37 | 0.207 | 0.020 | 0.227 | |
TSS.human.GRCh38 | 0.144 | 0.000 | 0.144 | |
TSS.human.NCBI36 | 0.111 | 0.004 | 0.114 | |
TSS.mouse.GRCm38 | 0.098 | 0.012 | 0.110 | |
TSS.mouse.NCBIM37 | 0.084 | 0.015 | 0.099 | |
TSS.rat.RGSC3.4 | 0.075 | 0.008 | 0.083 | |
TSS.rat.Rnor_5.0 | 0.069 | 0.004 | 0.073 | |
TSS.zebrafish.Zv8 | 0.078 | 0.004 | 0.081 | |
TSS.zebrafish.Zv9 | 0.087 | 0.008 | 0.095 | |
addAncestors | 1.069 | 0.052 | 1.122 | |
addGeneIDs | 0.958 | 0.044 | 1.002 | |
addMetadata | 1.079 | 0.092 | 1.171 | |
annoGR | 0 | 0 | 0 | |
annoPeaks | 3.985 | 0.236 | 4.817 | |
annotatePeakInBatch | 14.543 | 0.456 | 15.000 | |
annotatedPeak | 0.057 | 0.004 | 0.060 | |
assignChromosomeRegion | 0.001 | 0.000 | 0.000 | |
bdp | 0.001 | 0.000 | 0.000 | |
binOverFeature | 0.869 | 0.004 | 0.872 | |
binOverGene | 0.000 | 0.000 | 0.001 | |
binOverRegions | 0.000 | 0.000 | 0.001 | |
condenseMatrixByColnames | 0.013 | 0.000 | 0.012 | |
convert2EntrezID | 0.407 | 0.000 | 0.407 | |
countPatternInSeqs | 0.204 | 0.000 | 0.204 | |
cumulativePercentage | 0 | 0 | 0 | |
downstreams | 0.024 | 0.000 | 0.024 | |
egOrgMap | 0 | 0 | 0 | |
enrichedGO | 0.002 | 0.000 | 0.002 | |
enrichmentPlot | 0.568 | 0.008 | 0.576 | |
estFragmentLength | 0.000 | 0.000 | 0.001 | |
estLibSize | 0.001 | 0.000 | 0.001 | |
featureAlignedDistribution | 0.242 | 0.004 | 0.246 | |
featureAlignedExtendSignal | 0.001 | 0.000 | 0.001 | |
featureAlignedHeatmap | 0.378 | 0.008 | 0.387 | |
featureAlignedSignal | 0.32 | 0.02 | 0.34 | |
findEnhancers | 21.333 | 0.264 | 21.597 | |
findMotifsInPromoterSeqs | 13.464 | 0.270 | 13.743 | |
findOverlappingPeaks | 0.001 | 0.000 | 0.000 | |
findOverlapsOfPeaks | 1.767 | 0.008 | 1.774 | |
genomicElementDistribution | 0.001 | 0.000 | 0.001 | |
genomicElementUpSetR | 0.001 | 0.000 | 0.000 | |
getAllPeakSequence | 0.463 | 0.004 | 0.467 | |
getAnnotation | 0.001 | 0.000 | 0.000 | |
getEnrichedGO | 0.008 | 0.000 | 0.007 | |
getEnrichedPATH | 0.001 | 0.000 | 0.000 | |
getGO | 0 | 0 | 0 | |
getGeneSeq | 0.001 | 0.000 | 0.001 | |
getUniqueGOidCount | 0.001 | 0.000 | 0.001 | |
getVennCounts | 0.001 | 0.000 | 0.000 | |
hyperGtest | 0.001 | 0.000 | 0.001 | |
makeVennDiagram | 0.002 | 0.000 | 0.002 | |
mergePlusMinusPeaks | 0.000 | 0.000 | 0.001 | |
metagenePlot | 1.973 | 0.004 | 1.977 | |
myPeakList | 0.016 | 0.000 | 0.016 | |
oligoFrequency | 0.183 | 0.004 | 0.187 | |
oligoSummary | 0.000 | 0.000 | 0.001 | |
peakPermTest | 0.001 | 0.000 | 0.001 | |
peaksNearBDP | 0 | 0 | 0 | |
pie1 | 0.005 | 0.000 | 0.005 | |
plotBinOverRegions | 0.001 | 0.000 | 0.001 | |
preparePool | 0 | 0 | 0 | |
reCenterPeaks | 0.021 | 0.000 | 0.021 | |
summarizeOverlapsByBins | 5.930 | 0.417 | 6.066 | |
summarizePatternInPeaks | 0.553 | 0.032 | 0.586 | |
tileCount | 0.217 | 0.178 | 0.338 | |
tileGRanges | 0.138 | 0.125 | 0.038 | |
toGRanges | 0.103 | 0.007 | 0.112 | |
translatePattern | 0.000 | 0.001 | 0.001 | |
wgEncodeTfbsV3 | 0.218 | 0.010 | 0.228 | |
write2FASTA | 0.017 | 0.000 | 0.017 | |
xget | 0.116 | 0.016 | 0.131 | |